20-1724191-T-C

Variant names:

• chr20-1724191-T-C
• rs202516

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.514 in 151,994 control chromosomes in the GnomAD database, including 20,586 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (20586 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78132 AN: 151876 Hom.: 20560 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.471

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.514 AC: 78200 AN: 151994 Hom.: 20586 Cov.: 32 AF XY: 0.509 AC XY: 37803 AN XY: 74296

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.471

Alfa AF: 0.535 Hom.: 28715

Bravo AF: 0.522

Asia WGS AF: 0.390 AC: 1354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs202516; hg19: chr20-1704837;